When I was a kid playing TFTD I distinctively remember that moving through smoke tiles underwater adds +2 TU cost to all forms of movement. Moving diagonal cost 8, moving normal cost 6, and it may have been multiplied for above-4TU cost specialty tiles. It also causes no Stun underwater.
(On Land it behaved just like it does in ufo though)
I didnt make much use of smoke in TFTD because of that, I knew it took longer to move through it (annoyingly so) and I tried to skirt the edge as much as I could so that I could get a clear line of sight/fire to hit something. Only time that underwater soot ever helped was when I accidentally shot a pipeline and it filled a massive area with cover since it took awhile to move out of it.
Just the other day I was playing TFTD on my phone (android oxce+ 3.9 distro) and I noticed moving through the soot tiles underwater wasn't affecting my movement at all (it also caused stun accumulation), so this is a bug report.
Now im not so sure its a Good Idea to impose movement restriction from the smoke in an underwater enviro so it should probably be an Extended option to turn it off (just like leaving the Dye Grenade at 10 damage wasnt a good idea). Realistically being sooted-up sure grinds scuba operation to a crawl and can even cancel a dive early... but most of the time xcom agents have their feet planted on the seabed and remember the layout of what they saw before it went to gunk. And everybody underwater would be moving so slow that the timescale for every turn is absurdly longer than it would be on land.
I think this is a rule that could be implemented with whatever is designating a mission as being "underwater" (xcom agents wear helmets, they emit water bubbles, gunfire emits vapor trails, and explosion graphics default to bubble blasts) just to simplify things. I know Meridian updated his Enviros recently but I dont think thats the way to do it.